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Huang Q, Ng HQ, Loh YY, Ke Z, Lim WH, Kang C. Backbone 1H, 15N and 13C resonance assignments for an E2 ubiquitin conjugating enzyme-UBE2T. BIOMOLECULAR NMR ASSIGNMENTS 2023; 17:269-274. [PMID: 37773242 DOI: 10.1007/s12104-023-10154-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Ubiquitin-conjugating enzyme E2 T (UBE2T) plays important roles in ubiquitination of proteins through participation in transferring ubiquitin to its substrate. Due to its importance in protein modifications, UBE2T associates with diverse diseases and serves as an important target for drug discovery and development. The crystal structure of UBE2T has been determined and the structure reveals the lack of a druggable pocket for binding to small molecules for clinical applications. Despite the challenge, effort has been made to develop UBE2T inhibitors. We obtained UBE2T constructs with and without the C-terminal region which is flexible in solution. Herein, we report the backbone resonance assignments for human UBE2T without the C-terminal region. The backbone dynamics of UBE2T was also explored. The available assignments will be helpful for hit identification, determining ligand binding site and understanding the mechanism of action of UBE2T inhibitors.
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Affiliation(s)
- Qiwei Huang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Hui Qi Ng
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Yong Yao Loh
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Zhiyuan Ke
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Wan Hsin Lim
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore.
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Huang Q, Ng EY, Li Q, Kang C. 1 H, 15 N and 13 C resonance assignments of the Q61H mutant of human KRAS bound to GDP. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:51-56. [PMID: 34787842 DOI: 10.1007/s12104-021-10058-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
KRAS proteins are small GTPases binding to the cell membrane and playing important roles in signal transduction. KRAS proteins form complexes with GTP and GDP to result in active and inactive conformations favouring interactions with different proteins. Mutations in KRAS have impact on the GTPase activity and some mutants are related to certain types of cancers. In addition to mutation at position 12, the Q61H mutant is also identified as an oncogenic mutant. Here, we describe resonance assignment for Q61H mutant of human KRAS-4B. A construct containing 1-169 residues of KRAS with a point mutation at position 61 (Q to H) was made for solution NMR studies. The backbone and some side chain resonance assignments were obtained using conventional multi-dimensional experiments. The secondary structures were analysed based on the assigned residues. As NMR is a powerful tool in probing target and ligand interactions, the assignment will be useful for later compound binding studies.
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Affiliation(s)
- Qiwei Huang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, 05-01, 138670, Singapore
| | - Elizabeth Yihui Ng
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, 05-01, 138670, Singapore
| | - Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, 05-01, 138670, Singapore.
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Li Y, Zhong W, Koay AZ, Ng HQ, Nah Q, Wong YH, Hill J, Lescar J, Dedon PC, Kang C. Backbone resonance assignment for the full length tRNA-(N 1G37) methyltransferase of Pseudomonas aeruginosa. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:327-332. [PMID: 31175551 DOI: 10.1007/s12104-019-09900-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) plays important roles in translation, making it an important target for the development of new antibacterial compounds. TrmD comprises two domains with the N-terminal domain binding to the S-adenosyl-L-methionine (SAM) cofactor and the C-terminal domain critical for tRNA binding. Bacterial TrmD is functional as a dimer. Here we report the backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa. Most resonances were assigned and the secondary structure for each amino acid was determined according to the assigned backbone resonances. The availability of the assignment will be valuable for exploring molecular interactions of TrmD with ligands, inhibitors and tRNA.
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Affiliation(s)
- Yan Li
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, People's Republic of China
| | - Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Ann Zhufang Koay
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Hui Qi Ng
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Yee Hwa Wong
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jeffrey Hill
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - CongBao Kang
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore.
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Li Q, Ng HQ, Yoon HS, Kang C. Solution structure of the cyclic-nucleotide binding homology domain of a KCNH channel. J Struct Biol 2014; 186:68-74. [PMID: 24632450 DOI: 10.1016/j.jsb.2014.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/03/2014] [Accepted: 03/10/2014] [Indexed: 12/28/2022]
Abstract
The carboxy-terminal region of the KCNH family of potassium channels contains a cyclic-nucleotide binding homology domain (CNBHD) that is important for channel gating and trafficking. The solution structure of the CNBHD of the KCNH potassium of zebrafish was determined using solution NMR spectroscopy. This domain exists as a monomer under solution conditions and adopts a similar fold to that determined by X-ray crystallography. The CNBHD does not bind cAMP because residue Y740 blocks the entry of cyclic-nucleotide to the binding pocket. Relaxation results show that the CNBHD is rigid except that some residues in the loop between β6 and β7 are flexible. Our results will be useful to understand the gating mechanism of KCNH family members through the CNBHD.
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Affiliation(s)
- Qingxin Li
- Institute of Chemical & Engineering Sciences, Agency for Science, Technology and Research (A∗STAR), Singapore 627833, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A∗STAR), Singapore 138669, Singapore
| | - Ho Sup Yoon
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637511, Singapore
| | - Congbao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A∗STAR), Singapore 138669, Singapore.
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